This War That We Are In
by Tnmamabear2
Summary: Takes Place Directly following the Season Final (WILL CONTAIN SPOILERS) The team reflects on all the events that took place during the season final and prepare to move on with their life, but when the Mother Ship is stolen again and one of the team is missing, they find them selves in middle of yet another war.


**A/N: Thank You Jacqueline Roget for this suggestion. After reading your review and your suggestion for writing a post season final story, I started to jot down ideas I could do for the story and before I knew it I had the first chapter wrote! I hope you enjoy it!**

 **SPOLIER WARNING: This takes place directly following the ending of the Season Final. Please do not read if you haven't watched the Season Final. This story may contain some spoilers.**

Agent Christopher stood in the office where so many debriefings took place. She looked out the plate glass windows at the lifeboat charging. One more mission, one last time. She would be moving on come tomorrow, going to a new post somewhere. She smiled softly to herself, who would have ever thought a time machine and time travel was possible, or that a terrorist would steal it.

Terrorist...that was how she viewed Garcia Flynn, but it seemed Lucy was upset that he was arrested. She even started to have second thoughts about it when she over heard the conversation he had with Lucy. All he wanted was his family back. That was all he asked for. Unfortunately, he went about it the wrong way.

She was satisfied that she completed the job she was suppose to do. The mission was to bring in Garcia Flynn and that is what they did. The Mother ship would be returned to Mason Industries who already had the lifeboat back.

Now wasn't the time to second guess herself on weather she made the right call by following Lucy. She couldn't second guess on weather Garcia Flynn was really the bad guy. It turned out that everything he told them was true, everything about Rittenhouse and the evil they were involved in was all true. Rittenhouse was responsible for Flynn's family deaths and they framed him for it because he was a NSA agent who was getting a little too close to their operations.

Oh well, it was all over and done with now. She just had to leave this all behind her and make sure Mason had better security in place so no more time machines got stolen and they wouldn't have to travel down this road any more.

"We did it," Conner Mason said walking into the room, "We got our time machine back, we put a end to Rittenhouse and Garcia Flynn is in jail. It's all over with."

"Yeah, it is. Now, what are your plans for these Time Machines?" Agent Christopher asked him.

"Well, we are going with the original plan I had of doing some more experiment travels and then open it up for a tourist trip."

"I don't think time travel is for the public." She stated, "I don't believe this should ever be public knowledge. We have seen how the slightest change in space and time could destroy lives. I think it's your best option is to just destroy the machines. Who needs to travel back in time anyhow?"

"Someone who wants to visit a deceased family member. Someone who wishes they could change something might get the chance to. We could offer to deliver letters to people's younger selves so maybe they will make better choices." Mason stated, "This could be used for the good. We could try to prevent train crashes, plane crashes, terrorist attacks."

"You will be messing with history which you know could have a profound impact on the present. Things happened the way they did for a reason. It's best to let it be."

"I have to disagree, Agent." Conner shook his head, "Isn't there one thing in your life that you wish you had a chance to redo? Isn't there one time in your life when you just wished you could have known the outcome and you would have done things so much differently. One person you wished you could say good-bye too who you never got to see again."

Agent Christopher turned to hide the tears in her eyes. Conner was right, there was a lot she would change. People she would have said "I love you too" a little more often. People who she never got to say good bye too and missed even today.

"Yeah, yeah I do." she whispered, "but doesn't mean it's the right thing to do."

"You'd rather live the rest of your life with past regrets when you have a chance to change the past?"

"Changing the past would only give me different regrets. We can't get everything right all the time. We will always make mistakes and we will always have regrets. Even if we tried to change it, it's a never ending cycle. That's life."

"Sorry you feel that way, Agent Christopher. If you change your mind, look me up. I'll offer you a chance to change your past." he gave her a small smile before turning and walking away.

 **I I I**

Wyatt was looking at the lifeboat with a smile. It had been four wild months. It started out with him being half drunk when he first was brought into Mason and not caring about much of anything Then he found out about the time machine and had hope of bringing Jessica back and now here he was with a new outlook on life.

Fate was a funny thing. He wasn't meant to have Jessica back, but fate had brought Lucy into his life and threw them into a once in a life time situation that forced him to take a closer look at his feelings. It took him four months to get this far, to the point where he knew it was time to let Jessica go and to move on, explore other possibilities.

Lucy had asked him what those possibilities were and he told her he didn't know. He smiled to himself. He wanted to take this slow. He wanted to make sure he was making the right moves and the right choices. He needed to know she had the same feelings he did. Ever since the Alamo when she told him she needed him and trusted him, she had given him a whole new purpose for living. She was his reason for living. He had a sense to protect her. Not just on the job, but always. He wanted to be with her, he wanted to make her happy. He wanted to be her safe place to run.

He looked at his watch, she should be back any minute now and he would go with her to get Amy. He would get to meet this sister she had been talking about so much. He didn't have to go, but he wanted to go. He wanted to make sure she was safe. He wanted to spend time with her.

He should be heading back to base and getting a new mission and life goes on, but not this time. He wasn't ready to say good-bye to Lucy. He had a feeling that his life was right here with Lucy. He just had to get up the guts to tell her exactly what he was feeling and then let fate take it's course and see where things went from here.

 **I I I**

 _'Oh my God,' Lucy thought, my mother is Rittenhouse. She is just as bad as my father had been. Why did I never know? How could my mother not care about her younger daughter who was just erased from history? Does she not want Amy back? Did she never love Amy? Was it planned for me to be born, from two Rittenhouse members? What do they want from me now? Whatever it is, I WILL NOT DO IT. I am better then that. I am stronger then that. Rittenhouse ends with me._

 _'My mother said Rittenhouse already had an operative who has taken control of the mother ship. That means the mother ship is now in their control, and if what Anthony had told me was true, this country will be destroyed. We should have blown it up like Anthony wanted. I assumed Flynn killed him, but did Flynn really kill him or was it someone from Rittenhouse? I gotta get out of here, I gotta tell Wyatt and Denise. We've got to come up with a plan and stop Rittenhouse for good. Maybe I should have just allowed Flynn to blow up the summit. He was right all along. He was right about Rittenhouse killing his family and he was right about Rittenhouse having major plans for the mother ship, plans that surely would mean devastation.'_

"Are you saying you don't want Amy to come back?" Lucy asked softly as she pulled away from her mother's embrace.

"Oh honey...I don't know anything about this Amy. She was erased from history. Why in the world would I risk getting sick to have someone come back who I don't even remember? I can't care for someone who doesn't exist. You need to forget about her, she never existed."

"You never loved Amy, did you?" Lucy accused, her eyes filled with hurt. "Amy wasn't Rittenhouse and you didn't love her. She wasn't destined to take over the organization."

"Amy wasn't Rittenhouse, if she was, she would still be here. You...Lucy...you are like a princess. Your father and I are top Rittenhouse members. When he was arrested I assumed total control of the organization. He was number one and I was number two. It was only given that we would have a child together, a child who would be destined to become a Rittenhouse leader. You got rid of Flynn for us, Lucy, and now we will eliminate Mason Industries and all involved with them." Carolyn smiled.

"No...no...you won't." Lucy backed up. "I won't support this. I won't be a part of Rittenhouse. I will bring Rittenhouse down. You won't hurt anyone at Mason Industries if I can help it."

"Oh honey, I understand. I felt the same way and so did you father, but you don't understand the money and power involved with Rittenhouse. You don't know the good that comes of it. Give it time, and you will see. You will understand and you will be Rittenhouse's leader. You and Noah will be like King and Queen."

"No, won't be with Noah. I don't love him. We just broke things off. Noah appeared after I traveled. I don't have any memories of him and I can't make myself love him."

Carolyn laughed softly, "Honey, Noah and you have been planned to wed since birth. You both have very strong Rittenhouse backgrounds. Even if you don't marry him, all you have to do is have his child. The child that will be next in line for Rittenhouse. That is what you father and I did. We met and we had you, with plans of you becoming leader one day. That is what you and Noah will do. Have a pure blood Rittenhouse child."

"You're a monster! How can you support such things, mom? I thought I knew you! Don't you worry about what will be destroyed, what devastation will come to America and her people based on what Rittenhouse changes in the past or the future? Don't you care what will happen in the present?"

"It's too much for you to understand now, Sweetie, but only good will come from what Rittenhouse will do. Some people may not see it that way, but they don't understand what is good or bad. They elect government officials who don't have the best interest of the people in mind. People go places they shouldn't on vacation, they buy things they shouldn't, they watch TV programs they shouldn't, they have guns that they shouldn't. We will change all that. Rittenhouse will be fully in control and will control everything. People will be happier for it. They won't be able to make no more stupid choices because Rittenhouse will make the choices for them. As you grow in Rittenhouse you will see that everything that happens brings about good...such as this Amy you talk about...she was erased from the world and look, I am no longer sick. Good came from it. In time, you will see that too."

"No mom. I won't see that. I don't want any part of this." Lucy backed up to the door and hurried out of it, running to her car, tears stinging her eyes. Her world was falling apart. She thought the one constant thing in her life would be her mother, and now she finds her mother is no better then her biological father. What kind of woman wouldn't want one of her children back, regardless of the consequences! Lucy started the car and sped towards Mason Industries. She had to talk to Wyatt and Agent Christopher. They had to find a way to destroy the time machines.

 **I I I**

"Jiya? Jiya, what the hell just happened?" Rufus asked, terrified as Jiya seemed to be having some sort of seizure and pass out for a moment, then becoming normal again.

"I...I get a glimpse of the past, while in the present." she whispered, "Like, I was just looking out the window at the Bay Bridge and I got flashes of the bridge under construction. It's like I am in the past and present at the same time."

"We traveled to 1954, but the Golden Gate was built when, 1934 or so..."

"I don't understand it, either. I am fine one moment then I have these flashes of the past. This time it was a flash from what I was looking at. I don't know how it works or what is going on."

"It's because you were the fourth person in the time machine, and it was calibrated for only three people. Something got messed up. Sounds like part of you is here, but part of you is in the past."

"Kinda freaky, isn't it?" Jiya smiled softly.

"Scary." Rufus looked at her, his eyes full of fear, "Jiya, I don't want nothing to happen to you. I will never forgive myself. I love you..."

"I love you too. We will figure this out, maybe it will benefit us one day." she smiled softly as she caressed his face, "You kept me here, you kept me grounded when I didn't know what was happening to me back in 1954."

Rufus gave her a soft smile, "I promise to keep you safe, Jiya. Always and forever." he gave her a hug, "But I am going to have to leave here in a minute, I promised Lucy that I would pilot her back to 1979 to make sure her mother meets Henry Wallace so Amy will be back. That's our last mission. We are done after that. No more time travel." He smiled, "We go back to living a normal everyday life."

Jiya laughed softly, "Nothing is normal or ordinary about our life. It wasn't before the time machine and it won't be after all we have experienced."

"Ah, you got a point there. I for one, will not miss traveling back in time." He stated.

"I won't either. I thought it would be cool, but every time you left on a mission, I was always so afraid that you wouldn't come back." Jiya choked back her tears, "I almost lost you a few times."

"I know, but you kept me going. I just had to think of you and that gave me the strength to come back." Rufus kissed her softly. "I love you. I will see you soon."

"See you soon. Love ya." she smiled, watching him leave. So this was it. Everything was over. They got the mother ship back, Flynn was in jail, Lucy would get Amy back, and Rittenhouse members were all in jail. Life would return to normal again.

 **I I I**

"Wyatt..." Agent Christopher approached him.

"Yeah?" Wyatt turned around towards her with a smile, "Is the lifeboat ready? Lucy and Rufus should be here any minute now."

"We have a situation." Agent Christopher said softly. .

Wyatt's smile faded, a million thoughts running though his head. What had happened? Did Flynn escape? Did something happen to Lucy or her mother? Did Rittenhouse do something? "What. Is. It." he asked slowly, his body stiffening.

"Our agents who went to retrieve the mother ship have all been killed. We had ten agents go to retrieve it. They were found shot and the mother ship is gone." Agent Christopher said softly.

"Who in the hell could have taken it? Who knows how to operate the thing other then Rufus and...Emma..." Wyatt said.

"That's what we figure, but we don't know. No one can find Emma. She would have had to have help with her in order to take out all our men."

"Rittenhouse..." Wyatt muttered, "Flynn warned us and we didn't listen. Flynn had it right all along. Anthony even warned Lucy. He wanted to destroy the thing."

"Hey guys, what's up?" Rufus asked walking in.

Suddenly, Wyatt got a sinking feeling, "Where's Lucy?" he asked, looking at Rufus.

"I don't know. Not with me. I just got here. I've been with Jiya."

"She left to go somewhere. She knew the lifeboat would be charged in three hours. It's been almost three hours. She should be back by now or at least calling me." Wyatt grabbed his phone and tried calling Lucy. There was no answer.

"Something's happened." he stated, fear running though him, "I shouldn't have left her go alone."

"Wyatt, she might be in traffic. Let's not panic." Agent Christopher stated.

"Why are we panicking? What's happened?" Rufus asked.

"Rittenhouse has got the mother ship." Wyatt stated, "I am going to look for Lucy." he took off for the exit door driven by the overwhelming feeling that something had happened.

"If Lucy shows up, call me and keep her here!" Wyatt called before running out the door to his truck.

"Rittenhouse has the ship?" Rufus asked Agent Christopher.

"They could. We aren't exactly sure what happened or why. Only one we can think of who could operate the ship would be Emma."

"But she hid from Rittenhouse for ten years. Flynn went and got her..." Rufus frowned, "Does this mean Flynn is part of Rittenhouse? What about Lucy's journal? Her journal led Flynn to Emma, according to him."

"I don't know what to think or believe at this time." Agent Christopher said. "We will just have to wait and see what we can find out."

"Can't you see where the mother ship is now?" he asked.

"It's not as easy to track in present day. We normally only see when it travels to the past and returns. We have a team working on it though."

I I I

Wyatt figured Lucy would drive to her house to see her mother, knowing she might be sick when they returned, so that's the rout he took. He only went about four miles from Mason when he saw her car parked on the opposite side of the road. Wyatt spun his truck around and pulled up behind Lucy's car.

"Lucy?" he called running up to the car. He saw the flat tire, a spike sticking out of it. Lucy was no where in site. Her pocketbook was on the seat along with her cell phone. Her keys were still in the ignition.

"LUCY!" Wyatt yelled again, his heart pounding. Lucy was gone.

"I will get you back and I will kill the bastards who took you." Wyatt vowed. He wasn't going to lose another person he loved.

He dialed Agent Christopher's number, "They got Lucy." he said in a cold calm voice as soon as she answered. A voice that sent shivers down Agent Christopher's spin. Whoever had taken Lucy, she sure wouldn't want to be them once Wyatt got a hold of them.

"I know. We were able to track the mother ship to Daley City. We used Mason's NSA Database to try and capture who had the mother ship. We saw Emma and an unknown man. They had Lucy's hands handcuffed behind her back and held her at gun point." Agent Christopher paused, "She looked to be okay other then a gash on her head. We just pulled up the image when the mother ship left. They took Lucy with them."

"Where. To." Wyatt clenched his jaw and held his phone so tightly his knuckles were turning white.

"July 1, 1863 Pennsylvania." Denise answered.

"Battle of Gettysburg, the bloodiest battle of the civil war." Wyatt's blood ran cold. He feared facing another war scene, but what was worse then that, they had dragged Lucy in the middle of a war.

 **TBC**

 **Please take a moment to review and let me know what you think so far.**

 **I am open to any ideas or suggestions you would like to see.**


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